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Kasia Kedzierska
I am a PhD student at the University of Oxford. As a computational biologist, I use Data Science and Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression. Last summer, I joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I was working with NLP methods and knowledge graphs. Currently, I am looking into adapting my experience from the internship to build models for investigating cancer evolution.
Research Experience
Intern
Novo Nordisk Research Centre Oxford
Oxford, United Kingdom
2021
- I used NLP based methods to screen biomedical artciles and identify potential therapeutic targets. I built R Shiny App to allow colleagues within the company to investigate results from our pipeline.
DPhil Candidate
Wellcome Centre for Human Genetics, Big Data Institute
University of Oxford, UK
present - 2018
- In my PhD project Functional and evolutionary characterisation of chromatin organisation in endometrial cancer I am looking at how chromatin organisation influences disease progression in cancer of the uterus.
- Mentored by D. Church and D. Woodcock
- Currently I’m working on building and refining ML models of cancer evolution.
Visiting Graduate Student
Ratan group
University of Virginia, USA
2018 - 2017
- Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
- Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.
Visiting Graduate Student
Pemberton group
University of Virginia, USA
2017 - 2016
- Worked on Epigenetic regulation in prostate cancer.
- Performed experiments and analyzed data from RNA-seq, ATAC-seq, and ChIP-seq assays.
Research Assistant
Zebrafish Developmental Genomics
IIMCB, Warsaw, Poland
2016 - 2015
- I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
- I was responsible for both computational and experimental aspects of the project.
Education
DPhil. Candidate, Genomic Medicine and Statistics
Nuffield Department of Medicine, Brasenose College
University of Oxford, UK
present - 2018
- PhD fully funded by Wellcome Trust Four-year PhD Studentships in Science
M. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2018 - 2015
- Master thesis: - Analysis of the mutational burden across gene sets in cancer awarded the title of The Best Master Thesis in Bioinformatics defended in 2018.
B. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2015 - 2011
Publications
Discordant prognosis of mismatch repair deficiency in colorectal and endometrial cancer reflects variation in antitumour immune response and immune escape
Mark A Glaire, Neil AJ Ryan, Marieke E Ijsselsteijn, Katarzyna Kedzierska, Sofia Obolenski, Reem Ali, Emma J Crosbie, Tjalling Bosse, Noel Fcc De Miranda, David N Church
The Journal of pathology
2022
Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift
M. Migdal, E. Tralle, K. A. Nahia, L. Bugajski, K. Z. Kedzierska, F. Garbicz, K. Piwocka, C. L. Winata, M. Pawlak
BMC Genomics
2021
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis
Clinical Epigenetics
2020
Prognostic integrated image-based immune and molecular profiling in early-stage Endometrial Cancer
N. Horeweg, M. de Bruyn, R. A. Nout, E. Stelloo, K. Kedzierska, A. León-Castillo, A. Plat, K. D. Mertz, M. Osse, I. M. Jürgenliemk-Schulz, L. C.H.W. Lutgens, J. J. Jobsen, E. M. van der Steen-Banasik, V. T. Smit, C. L. Creutzberg, T. Bosse, H. W. Nijman, V. H. Koelzer and D. N. Church
Cancer Immunology Research
2020
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata
Genome Research
2019
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
K. Jividen, K. Z. Kedzierska, C.-S. Yang, K. Szlachta, A. Ratan and B. M. Paschal
BMC Cancer
2018
SONiCS: PCR stutter noise correction in genome-scale microsatellites
K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler
Bioinformatics
2018
Posters, and Talks
Systematic characterisation of chromatin modifiers in endometrial cancer
European Association for Cancer Research 2022 Congress
Seville, Spain
2022
Analysis of the mutational burden across gene sets in cancer
Polish Bioinformatics Society Symposium
Cracow, Poland
2019
- Invited talk
Differential mutation analysis across gene sets in cancers
Cold Spring Harbor, NY, USA
2018
- Poster
Epigenetic regulation of prostate cancer
Visiting Graduate Traineeship Program Grantees Symposium
Charlottesville, VA, USA
2017
- Talk
Awards and honours
Senior Hulme Scholarship
Brasenose College, University of Oxford
Oxford, UK
present - 2021
- Senior Hulme Scholarship is awarded by Brasenose College, University of Oxford to DPhil students whose academic performance is deemed to be exceptional.
Graduate Prize in the ‘Outstanding work outside degree’ category
Nuffield Department of Medicine, University of Oxford
Oxford, UK
2022 - 2021
- Each year Nuffield Department of Medicine, based on nominations, awards selected PhD students based on their performance within and outside of their degree.
Best Master Thesis in Bioinformatics
Polish Bioinformatics Society
Poland
2019 - 2018
- Analysis of the mutational burden across gene sets in cancer - Best Master Thesis defended in Bioinformatics in 2018 in Poland.
Visiting Graduate Traineeship Program, now known as BioLAB
Fulbright Poland
University of Virginia, VA, USA
2017 - 2016
- The Visiting Research Graduate Traineeship Program offered 12-month research traineeships for outstanding, qualified students from the life sciences at selected institutions in the United States.
Grasz o Staz
PwC Poland
Poland
2015
- “Grasz o Staz” competition was a national, prestigious and highly competitive (1:25 success rate) scholarship program in Poland organized by PwC.
Teaching Experience
Unsupervised learning
NGSchool2022: Machine Learning in Computational Biology
Jablonna, Poland
2022
- I co-led, with Kaspar Märtens, lecture and tutorial sessions on unsupervised learning and its use cases in computational biology. All materials are availble at github.com/kzkedzierska/ngs22_unsupervised.
Data visualization in bioinformatics - hackathon mentor
Online hackathon NGSprint
Discord
2021
- I led the hackathon in data viusalisation with emphasis on computational biology. Under my supervision, 3 teams of around 5 people each, created interactive and captivating visualisation. Teaching materials are available at github.com/kzkedzierska/NGSprint_data_viz.
Online tutorials: Python for Data Science and Introduction to Python
YouTube
2020
- I led two Python tutorials: Introduction to Python kasia.codes/talk/intro_to_python/ and Python for Data Science kasia.codes/talk/py4ds/.
Unsupervised learning, Introduction to Python
#NGSchool2019: Machine Learning for Biomedicine
Ostróda, Poland
2019
- Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
- Materials for the Introduction to Python are available on github
Introduction to R
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2019
- 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
- Materials available on github/kzkedziersa/r_intro
Introduction to Managing Code with Git
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2020 - 2019
- I led a 2-hour introduction to working with Git. Materials, including slides and exercises are available at kasia.codes/talk/into_to_git/.
ATAC-seq workshop
#NGSchool2017: Single-cell Sequencing
Jachranka, Poland
2017
- Invited speaker
- Materials for the course can be available on gitub.com/kzkedzierska/ATACseq_workshop
Attended Workshops, Summer Schools
Machine Learning Summer School
Imperial College London, University College London
London, United Kingdom
2019
Grants
Visegrad Grant to organize #NGSchool2020 postponed until 2022
N/A
2022 - 2020
- 32,190 EUR awarded towards organising affordable training and conference focusing on ML application in Computational Biology. During this project I managed an international team of 9 people and led the organisation of summer school, conference, online seminars and hackathon.
Visegrad Grant to organize #NGSchool2019
N/A
2019
- 23,500 EUR awarded towards organising #NGSchool2019 allowed to keep the cost of attenting the school to the minimum and record the lectures for broader access.
Non profit work
President
N/A
2022 - 2018
- The goal of the Society is to promote and support science, with emphasis on computational biology.
- President since 2019; Vice President 2018 - 2019, Founder